What is hg19/hg38? - All you need to know about human reference genomes | Bioinformatics 101

In this video I go over what are reference genomes, how are they build and what are some uses of having a reference genome. In addition, I talk about what are different builds (versions) of reference genomes i.e. GRCh38 (hg38)/GRCh37, what makes them different and which one should be used to perform genomics analysis.
I hope you find this video helpful! Leave your thoughts in the comment section below!
Chapters:
0:00 Intro
0:31 What is a reference genome?
1:41 Human reference genome is NOT...
2:05 Why sequence full human genome?
3:24 How is a human reference genome created?
5:08 Reference genome builds (versions)
6:22 What's with multiple names - GRCh37, hg19 or b37?
7:21 Types of sequences found in a human reference fasta file
8:24 What are alternate loci?
10:13 GRCh37 (hg19) vs GRCh38 (hg38) - which one should I use?
10:56 Visualizing a gene in both versions of reference genome in IGV
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To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: [e-mail]
#bioinformagician #bioinformatics #hg38 #hg19 #grch38 #denovoassemby #grch37 #sequencing #coverage #samtools #depthofsequencing #samflag #sam #bam #alignment #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs

[@kevinsho2601]

This channel is goldmine. I have a health startup and have used so many resources to learn bioinformatics because we are using omics technologis. This is one of the only sources that removes some ambiguity from ambiguous subject matter. I see a lot of good biology channels fall off and discontinue videos. I hope this is not one of them.

[@abhayrastogi590]

Thanks a lot for making these videos!

[@anmolpardeshi3138]

this is an awesome video! Kudos to your efforts!

[@ashaypatel7523]

your work is amazing, thank you so much! 🙏

[@user-jl4jv3yc3e]

Hey! very nice video and very informative!! I just wanted to ask that is it admissible that to use primary assembly with softmasking(.sm) and repeated masking (.rm) file for rna seq? If so which one we should prefer.. .sm or .rm or only primary assembly file

[@ravimore5786]

Awesome 👍

[@Ice84letters]

Hellow! thank you so much for the videos!! are there a video on how to use liftover with command lines from hg19 to hg38? thanks a lot!!!

[@MariMari-sw1cr]

Thank you so much for all your effort. You cannot imagine how much your videos helped me. However, I would appreciate it if you could make a video about visualizing NGS data with R. Thank you again!

[@Bioinformagician]

I will surely plan on making videos covering that!

[@anshikadutta359]

Hi khusbu, I will be completing my master's in CSE under nlp as specialization... But know m getting very much fasinated in the field of bioinformatics... So, what all preparation and sources needed inorder to get this for a cse student , what are its scope on further run..

[@Bioinformagician]

I have a guest speaker on my channel who has talked about all things bioinformatics, starting with what this field entails, how can one prepare and get into this field, what is the scope and opportunities in this area. I recommend you to watch that - kzbin.info/www/bejne/o5utmWeggMhoj5Y

[@anshikadutta359]

Thank You ..

[@ZohiraTalks]

Thanks a lot❤

[@simrankang3082]

Thank you. Could you please make a video on how to use liftover from hg19 to hg38.

[@Bioinformagician]

Sure, will add it to my list. Thanks for the suggestion.

[@shreyajohnson2589]

Can T2T reference be as good as hg38 or better than it?

[@aiswaryanair9033]

Hai can you point to sone reading material WRT to this?

[@aiswaryanair9033]

* some

[@Bioinformagician]

Here you go: 1. gatk.broadinstitute.org/hc/en-us/articles/360035891071-Reference-genome 2. gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19 3. www.hudsonalpha.org/sequencing-from-scratch-reference-genomes-and-de-novo-sequence-assembly/ 4. genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1774-4

[@SaniyaKhullar]

Thanks for the video. Please note this video to convert from hg19 to hg38 (or vice-versa): kzbin.info/www/bejne/b2WViH-frpiYmJY.